-
Proceedings
M. van der Kolk, C. Miller, R. Padmos, V. Azizi, and A. Hoekstra.
des-ist: A Simulation Framework to Streamline Event-Based In Silico Trials.
In:
Computational Science – ICCS 2021.
ISBN
9783030779672.
III, pp. 648-654.
-
Article
D. Groen, H. Arabnejad, V. Jancauskas, W. N. Edeling, F. Jansson, R. A. Richardson, J. Lakhlili, L. Veen, B. Bosak, P. Kopta, D. W. Wright, N. Monnier, P. Karlshoefer, D. Suleimenova, R. Sinclair, M. Vassaux, A. Nikishova, M. Bieniek, O. O. Luk, M. Kulczewski, E. Raffin, D. Crommelin, O. Hoenen, D. P. Coster, and P. V. Coveney.
VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations.
Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences
379(2197), 20200221.
-
Article
Loes Crielaard, Mary Nicolaou, Alexia Sawyer, Rick Quax, and Karien Stronks.
Understanding the impact of exposure to adverse socioeconomic conditions on chronic stress from a complexity science perspective.
BMC Medicine
19(1).
-
Article
D. Ye, L. Veen, A. Nikishova, J. Lakhlili, W. Edeling, O. O. Luk, V. V. Krzhizhanovskaya, and A. G. Hoekstra.
Uncertainty quantification patterns for multiscale models.
Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences
379(2197), 20200072.
-
Proceedings
C. Miller, M. van der Kolk, R. Padmos, T. Józsa, and A. Hoekstra.
Uncertainty Quantification of Coupled 1D Arterial Blood Flow and 3D Tissue Perfusion Models Using the INSIST Framework.
In:
Computational Science – ICCS 2021.
ISBN
9783030779801.
VI, pp. 691-697.
-
Article
S. Achterhof and J. M. Meylahn.
Two-community noisy Kuramoto model with general interaction strengths. II.
Chaos
31(3), 033116.
-
Article
S. Achterhof and J. M. Meylahn.
Two-community noisy Kuramoto model with general interaction strengths. I.
Chaos
31(3), 033115.
-
Proceedings
R. M. Padmos, T. I. Józsa, W. K. El-Bouri, G. Závodszky, S. J. Payne, and A. G. Hoekstra.
Two-Way Coupling Between 1D Blood Flow and 3D Tissue Perfusion Models.
In:
Computational Science – ICCS 2021.
ISBN
9783030779672.
III, pp. 670-683.
-
Article
D. Suleimenova, H. Arabnejad, W. N. Edeling, D. Coster, O. O. Luk, J. Lakhlili, V. Jancauskas, M. Kulczewski, L. Veen, D. Ye, P. Zun, V. Krzhizhanovskaya, A. Hoekstra, D. Crommelin, P. V. Coveney, and D. Groen.
Tutorial applications for Verification, Validation and Uncertainty Quantification using VECMA toolkit.
Journal of Computational Science
53, 101402.
-
Article
UnYoung Chavez-Baldini, Dorien H Nieman, Amos Keestra, Anja Lok, Roel J T Mocking, Pelle de Koning, Valeria V Krzhizhanovskaya, Claudi L H Bockting, Geeske van Rooijen, Dirk J A Smit, Arjen L Sutterland, Karin J H Verweij, Guido van Wingen, Johanna T W Wigman, Nienke C Vulink, and Damiaan Denys.
The relationship between cognitive functioning and psychopathology in patients with psychiatric disorders.
Psychological Medicine
.
-
Article
W. Edeling, H. Arabnejad, R. Sinclair, D. Suleimenova, K. Gopalakrishnan, B. Bosak, D. Groen, I. Mahmood, D. Crommelin, and P. V. Coveney.
The impact of uncertainty on predictions of the CovidSim epidemiological code.
Nature Computational Science
1(2), pp. 128-135.
-
Article
C. J. Spieker, G. Závodszky, Clarisse Mouriaux, Max van der Kolk, Christian Gachet, Pierre H. Mangin, and A. G. Hoekstra.
The Effects of Micro-vessel Curvature Induced Elongational Flows on Platelet Adhesion.
Annals of Biomedical Engineering
.
-
Article
I. S. Kleinwächter, S. Pannwitt, A. Centi, N. Hellmann, E. Thines, T. Bereau, and D. Schneider.
The Bacteriostatic Activity of 2-Phenylethanol Derivatives Correlates with Membrane Binding Affinity.
Membranes
11(4), 254.
-
Report
Leesa Quinlan, Martin Reeves, David Purser, Simon Levin, and V. V. Vasconcelos.
Strategies of Change.
-
Article
P. Rutten, M. H. Lees, S. Klous, and P. M. A. Sloot.
State-space models reveal bursty movement behaviour of dance event visitors.
EPJ Data Science
10(35), 35.
-
Article
J. Bruggeman, R. Sprik, and R. Quax.
Spontaneous cooperation for public goods.
Journal of Mathematical Sociology
45(3), pp. 183-191.
-
Article
M. Bause and T. Bereau.
Reweighting non-equilibrium steady-state dynamics along collective variables.
Journal of Chemical Physics
154(13), 134105.
-
Article
Tamás I. Józsa, R. M. Padmos, Wahbi K. El-Bouri, A. G. Hoekstra, and Stephen J. Payne.
On the Sensitivity Analysis of Porous Finite Element Models for Cerebral Perfusion Estimation.
Annals of Biomedical Engineering
.
-
Article
D. Ye, A. Nikishova, L. Veen, P. Zun, and A. G. Hoekstra.
Non-intrusive and semi-intrusive uncertainty quantification of a multiscale in-stent restenosis model.
Reliability Engineering & System Safety
214, 107734.
-
Article
R. M. Padmos, N. Arrarte Terreros, T. I. Józsa, G. Závodszky, H. A. Marquering, C. B. L. M. Majoie, and A. G. Hoekstra.
Modelling the leptomeningeal collateral circulation during acute ischaemic stroke.
Medical Engineering & Physics
91, pp. 1-11.
-
PhD Thesis
M. Bause.
Maximum caliber approach to reweight dynamics of non-equilibrium steady states.
Supervised by T. Bereau and E. J. Meijer.
-
Article
J. F. Uleman, R. J. F. Melis, R. Quax, E. A. van der Zee, D. Thijssen, M. Dresler, O. van de Rest, I. F. van der Velpen, H. H. H. Adams, B. Schmand, I. M. C. M. de Kok, J. de Bresser, E. Richard, M. Verbeek, A. G. Hoekstra, E. A. J. A. Rouwette, and M. G. M. Olde Rikkert.
Mapping the multicausality of Alzheimer’s disease through group model building.
GeroScience
43(2), p. 829–843.
-
Article
P. Rutten, M. H. Lees, S. Klous, and P. M. A. Sloot.
Intermittent and persistent movement patterns of dance event visitors in large sporting venues.
Physica A : Statistical Mechanics and its Applications
563, 125448.
-
Article
B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, and D. N. Ku.
Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study.
Interface Focus
11(1), 20190126.
-
Article
C. E. S. Mattsson, F. W. Takes, E. M. Heemskerk, C. Diks, G. Buiten, A. Faber, and P. M. A. Sloot.
Functional Structure in Production Networks.
Frontiers in Big Data
4, 666712.
-
Article
Martin Girard and Tristan Bereau.
Finite-size transitions in complex membranes.
Biophysical Journal
120(12), pp. 2436-2443.
-
Article
E. Weinans, R. Quax, E. H. van Nes, and I. A. van de Leemput.
Evaluating the performance of multivariate indicators of resilience loss.
Scientific Reports
11, 9148.
-
Article
J. Kwak, M. H. Lees, W. Cai, A. R. Pourghaderi, and M. E. H. Ong.
Estimating horizontal movement performance of patient beds and the impact on emergency evacuation time.
Safety Science
134, 105038.
-
Article
J. F. Rudzinski, S. Kloth, S. Wörner, T. Pal, K. Kremer, T. Bereau, and M. Vogel.
Dynamical properties across different coarse-grained models for ionic liquids.
Journal of Physics-Condensed Matter
33(22), 224001.
-
Proceedings
Dennis Knol, Fons de Leeuw, Jan Fokke Meirink, and Valeria V. Krzhizhanovskaya.
Deep Learning for Solar Irradiance Nowcasting: A Comparison of a Recurrent Neural Network and Two Traditional Methods.
In:
Computational Science – ICCS 2021 - 21st International Conference, Proceedings.
ISBN
9783030779764.
V, pp. 309-322.
-
Article
A. Dutta, J. Vreeken, L. M. Ghiringhelli, and T. Bereau.
Data-driven equation for drug-membrane permeability across drugs and membranes.
Journal of Chemical Physics
154(24), 244114.
-
Article
R. M. Padmos, T. I. Józsa, W. K. El-Bouri, P. R. Konduri, S. J. Payne, and A. G. Hoekstra.
Coupling one-dimensional arterial blood flow to three-dimensional tissue perfusion models for in silico trials of acute ischaemic stroke.
Interface Focus
11(1), 20190125.
-
Article
V. S. Muniraj.
Continuous clonal labeling reveals uniform progenitor potential in the adult exocrine pancreas.
Cell Stem Cell
.
-
Article
Martin Girard and Tristan Bereau.
Computer simulations of lipid regulation by molecular semigrand canonical ensembles.
Biophysical Journal
120(12), pp. 2370-2373.
-
PhD Thesis
-
Proceedings
V. S. Muniraj and P. M. A. Sloot.
Computational modeling of the post-burn immune response.
In:
International Society for Burn Injuries.
-
Article
W. Sun, L. Liu, X. Chen, A. Szolnoki, and V. V. Vasconcelos.
Combination of institutional incentives for cooperative governance of risky commons.
iScience
24(8), 102844.
-
Article
F. P. Santos, S. A. Levin, and V. V. Vasconcelos.
Biased perceptions explain collective action deadlocks and suggest new mechanisms to prompt cooperation.
iScience
24(4), 102375.
-
Article
M. Stieffenhofer, T. Bereau, and M. Wand.
Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability.
APL Materials
9(3), 031107.
-
Article
Junus van der Wal, C. D. van Borkulo, M. K. Deserno, J. J. F. Breedvelt, Michael Lees, J. C. Lokman, D. Borsboom, Damiaan Denys, Ruth J van Holst, M. P. Smidt, K. Stronks, P. J. Lucassen, J. C. M. van Weert, P. M. A. Sloot, C. L. Bockting, and R. W. Wiers.
Advancing urban mental health research: from complexity science to actionable targets for intervention.
The Lancet. Psychiatry
8(11).
-
Article
V. A. Karatayev, V. V. Vasconcelos, A.-S. Lafuite, S. A. Levin, C. T. Bauch, and M. Anand.
A well-timed shift from local to global agreements accelerates climate change mitigation.
Nature Communications
12, 2908.
-
Article
A. Presbitero, V. R. Melnikov, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
A unifying model to estimate the effect of heat stress in the human innate immunity during physical activities.
Scientific Reports
11, 16688.
-
Article
T. I. Józsa, R. M. Padmos, N. Samuels, W. K. El-Bouri, A. G. Hoekstra, and S. J. Payne.
A porous circulation model of the human brain for in silico clinical trials in ischaemic stroke.
Interface Focus
11(1), 20190127.
-
Article
-
Article
D. Roy and M. Lees.
Understanding resilience in slums using an agent-based model.
Computers, Environment and Urban Systems
80, 101458.
-
PhD Thesis
A. Nikishova.
Uncertainty quantification of multiscale models.
ISBN
9789402819182.
Supervised by
A. G. Hoekstra and P. V. Coveney.
-
Article
B. Czaja, M. Gutierrez, G. Závodszky, D. de Kanter, A. Hoekstra, and O. Eniola-Adefeso.
The influence of red blood cell deformability on hematocrit profiles and platelet margination.
PLoS Computational Biology
16(3), e1007716.
-
Article
-
Article
L. Crielaard, P. Dutta, R. Quax, M. Nicolaou, N. Merabet, K. Stronks, and P. M. A. Sloot.
Social norms and obesity prevalence: From cohort to system dynamics models.
Obesity Reviews
21(9), e13044.
-
Article
A. Nikishova, G. E. Comi, and A. G. Hoekstra.
Sensitivity analysis based dimension reduction of multiscale models.
Mathematics and Computers in Simulation
170, pp. 205-220.
-
Proceedings
I. Derevitskii, N. Kogtikov, M. H. Lees, W. Cai, and M. E. H. Ong.
Risk-based AED placement - Singapore case.
In:
Computational Science – ICCS 2020.
ISBN
9783030504236.
IV, pp. 577-590.
-
PhD Thesis
I. Anagnostou.
Risk management in trading activities through the lens of complex systems theory.
ISBN
9789464211009.
Supervised by
B. D. Kandhai and A. G. Hoekstra.
-
Article
M. Girard and T. Bereau.
Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms.
Biophysical Journal
119(5), pp. 892-899.
-
Article
M. Boersma, A. Maliutin, S. Sourabh, L. A. Hoogduin, and D. Kandhai.
Reducing the complexity of financial networks using network embeddings.
Scientific Reports
10, 17045.
-
Article
A. M. Shibeko, B. Chopard, A. G. Hoekstra, and M. A. Panteleev.
Redistribution of TPA Fluxes in the Presence of PAI-1 Regulates Spatial Thrombolysis.
Biophysical Journal
119(3), pp. 638-651.
-
Article
O. Har-Shemesh, R. Quax, J. S. Lansing, and P. M. A. Sloot.
Questionnaire data analysis using information geometry.
Scientific Reports
10, 8633.
-
Article
S. Sourabh, Markus Hofer, and B. D. Kandhai.
Quantifying systemic risk using Bayesian networks.
Risk.net
.
-
Article
A. H. R. Koch, S. Morsbach, T. Bereau, G. Lévêque, H.-J. Butt, M. Deserno, K. Landfester, and G. Fytas.
Probing Nanoparticle/Membrane Interactions by Combining Amphiphilic Diblock Copolymer Assembly and Plasmonics.
The journal of Physical Chemistry. B
124(5), pp. 742-750.
-
PhD Thesis
B. J. M. van Rooij.
Platelet adhesion and aggregation in high shear blood flow.
ISBN
9789402820287.
Supervised by
A. G. Hoekstra and G. Závodszky.
-
Article
C. Hoffmann, A. Centi, R. Menichetti, and T. Bereau.
Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations.
Scientific Data
7, 51.
-
Proceedings
J. Kwak, M. H. Lees, W. Cai, and M. E. H. Ong.
Modeling helping behavior in emergency evacuations using volunteer’s dilemma game.
In:
Computational Science – ICCS 2020.
ISBN
9783030503710.
I, pp. 513-523.
-
PhD Thesis
V. Sivadasan.
Microstructure dynamics in shear thickening suspensions.
ISBN
9789402818611.
Supervised by
A. G. Hoekstra and D. Bonn.
-
Article
O. Severiukhina, S. Kesarev, K. Bochenina, A. Boukhanovsky, M. H. Lees, and P. M. A. Sloot.
Large-scale forecasting of information spreading.
Journal of Big Data
7, 72.
-
Article
C. Scherer, R. Scheid, D. Andrienko, and T. Bereau.
Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids.
Journal of Chemical Theory and Computation
16(5), pp. 3194-3204.
-
Article
K. de Vries, A. Nikishova, B. Czaja, G. Závodszky, and A. G. Hoekstra.
Inverse Uncertainty Quantification of a cell model using a Gaussian Process metamodel.
International Journal for Uncertainty Quantification
10(4), pp. 333-349.
-
Article
A. Centi, A. Dutta, S. H. Parekh, and T. Bereau.
Inserting Small Molecules across Membrane Mixtures.
Biophysical Journal
118(6), pp. 1321-1332.
-
Article
P. R. Konduri, H. A. Marquering, E. E. van Bavel, A. Hoekstra, C. B. L. M. Majoie, R. Padmos, and V. Azizi.
In-Silico Trials for Treatment of Acute Ischemic Stroke.
Frontiers in Neurology
11, 558125.
-
Article
O. Metsker, K. Magoev, A. Yakovlev, S. Yanishevskiy, G. Kopanitsa, S. Kovalchuk, and V. V. Krzhizhanovskaya.
Identification of risk factors for patients with diabetes: diabetic polyneuropathy case study.
BMC Medical Informatics and Decision Making
20, 201.
-
Article
B. Csippa, D. Gyürki, G. Závodszky, I. Szikora, and G. Paál.
Hydrodynamic Resistance of Intracranial Flow-Diverter Stents.
Cardiovascular Engineering and Technology
11(1), pp. 1-13.
-
Article
C. Rauer and T. Bereau.
Hydration free energies from kernel-based machine learning: Compound-database bias.
Journal of Chemical Physics
153(1), 014101.
-
Article
C. Liu, J. G. Brandenburg, O. Valsson, K. Kremer, and T. Bereau.
Free-energy landscape of polymer-crystal polymorphism.
Soft Matter
16(42), pp. 9683-9692.
-
Article
J. J. Lever, I. A. van de Leemput, E. Weinans, R. Quax, V. Dakos, E. H. van Nes, J. Bascompte, and M. Scheffer.
Foreseeing the future of mutualistic communities beyond collapse.
Ecology Letters
23(1), pp. 2-15.
-
Article
M. V. Sheraton, G. G. Y. Chiew, V. Melnikov, E. Y. Tan, K. Q. Luo, N. Verma, and P. M. A. Sloot.
Emergence of spatio-temporal variations in chemotherapeutic drug efficacy: in-vitro and in-Silico 3D tumour spheroid studies.
BMC Cancer
20, 1201.
-
Proceedings
L. E. Veen and A. G. Hoekstra.
Easing Multiscale Model Design and Coupling with MUSCLE 3.
In:
Computational Science – ICCS 2020.
ISBN
9783030504335.
VI, pp. 425-438.
-
Proceedings
B. Nannes, R. Quax, H. Ashikaga, M. Hocini, R. Dubois, O. Bernus, and M. Haïssaguerre.
Early signs of critical slowing down in heart surface electrograms of ventricular fibrillation victims.
In:
Computational Science – ICCS 2020.
ISBN
9783030504236.
IV, pp. 334-347.
-
Proceedings
A. Presbitero, R. Quax, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
Detecting critical transitions in the human innate immune system post-cardiac surgery.
In:
Computational Science – ICCS 2020.
ISBN
9783030503710.
I, pp. 371-384.
-
Article
J. W. Barnett, C. R. Bilchak, Y. Wang, B. C. Benicewicz, L. A. Murdock, T. Bereau, and S. K. Kumar.
Designing exceptional gas-separation polymer membranes using machine learning.
Sciences advances
6(20), eaaz4301.
-
Article
C. H. Tan, H.-S. Oh, V. M. Sheraton, E. Mancini, S. C. J. Loo, S. Kjelleberg, P. M. A. Sloot, and S. A. Rice.
Convection and the Extracellular Matrix Dictate Inter- and Intra-Biofilm Quorum Sensing Communication in Environmental Systems.
Environmental Science and Technology
54(11), p. 6730–6740.
-
Article
I. Anagnostou, J. Sanchez Rivero, S. Sourabh, and D. Kandhai.
Contagious defaults in a credit portfolio: a Bayesian network approach.
Journal of Credit Risk
16(1), pp. 1-26.
-
Article
P. J. S. Cardoso, J. M. F. Rodrigues, J. Monteiro, R. Lam, V. V. Krzhizhanovskaya, M. H. Lees, J. Dongarra, and P. M. A. Sloot.
Computational Science in the Interconnected World: Selected papers from 2019 International Conference on Computational Science.
Journal of Computational Science
47, 101222.
-
Article
J. F. Rudzinski and T. Bereau.
Coarse-grained conformational surface hopping.
Journal of Chemical Physics
153(21), 214110.
-
PhD Thesis
B. E. Czaja.
Cell resolved blood flow modeling with the Lattice Boltzmann method.
ISBN
9789464211191.
Supervised by
A. G. Hoekstra and G. Závodszky.
-
Article
D. W. Wright, R. A. Richardson, W. Edeling, J. Lakhlili, R. C. Sinclair, V. Jancauskas, D. Suleimenova, B. Bosak, M. Kulczewski, T. Piontek, P. Kopta, I. Chirca, H. Arabnejad, O. O. Luk, O. Hoenen, J. Węglarz, D. Crommelin, D. Groen, and P. V. Coveney.
Building Confidence in Simulation: Applications of EasyVVUQ.
Advanced Theory and Simulations
3(8), 1900246.
-
Article
J. Burger, D. C. van der Veen, D. J. Robinaugh, R. Quax, H. Riese, R. A. Schoevers, and S. Epskamp.
Bridging the gap between complexity science and clinical practice by formalizing idiographic theories: a computational model of functional analysis.
BMC Medicine
18, 99.
-
Article
B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, and D. N. Ku.
Biorheology of occlusive thrombi formation under high shear: in vitro growth and shrinkage.
Scientific Reports
10, 18604.
-
Article
D. Roy, D. Bernal, and M. Lees.
An exploratory factor analysis model for slum severity index in Mexico City.
Urban Studies
57(4), pp. 789-805.
-
Article
P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, and A. G. Hoekstra.
A particle-based model for endothelial cell migration under flow conditions.
Biomechanics and Modeling in Mechanobiology
19(2), pp. 681-692.
-
Article
G. Závodszky, B. Csippa, G. Paál, and I. Szikora.
A novel virtual flow diverter implantation method with realistic deployment mechanics and validated force response.
International Journal for Numerical Methods in Biomedical Engineering
36(6), e3340.
-
Article
J. R. Helmus, M. H. Lees, and R. van den Hoed.
A data driven typology of electric vehicle user types and charging sessions.
Transportation Research. Part C, Emerging Technologies
115, 102637.
-
Proceedings
B. Czaja, G. Závodszky, and A. Hoekstra.
A Heterogeneous Multi-scale Model for Blood Flow.
In:
Computational Science – ICCS 2020.
ISBN
9783030504335.
VI, pp. 403-409.
-
Article
Publications of the CSL group